The Nature of Interactions in the Ionic Crystal of 3-Pentenenitrile, 2-Nitro-5-oxo, Ion(−1), Sodium

Góra, Robert W.; Sokalski, W. Andrzej; Leszczyński, Jerzy; Pett, Virginia B.

doi:10.1021/jp046912v

Cited by 39 publications

(44 citation statements)

References 49 publications

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“…, and the charges transfer between the N 5 ? unit and the coordinated anions are 0.04-0.28 e. A better understanding of the changes in the electronic structure can be derived from the inspection of the difference density map [44]. Take N 5 A S F 6 for example, Fig.…”

Section: Resultsmentioning

confidence: 99%

DFT studies on the structures and stabilities of N5 +-containing salts

Wang

Zhang

et al. 2011

Struct Chem

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Density functional theory (DFT) methods have been applied to study the properties of series of N 5 ? salts. The thermal stabilities of the crystals are evaluated based on the reaction enthalpy (DH) and free energy change (DG) of the salts when they dissociate into neutral products. The energy outputs of salts in explosion indicate that all N 5 ? salts yield large energy except for N 5 SbF 6 and N 5 Sb 2 F 11 . Considering the released energy and thermal stability, (N 5 ) 2 SnF 6 , N 5 PF 6 , N 5 BF 4 , and N 5 SO 3 F may be potential candidates of very energetic explosives.

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Section: Resultsmentioning

confidence: 99%

DFT studies on the structures and stabilities of N5 +-containing salts

Wang

Zhang

et al. 2011

Struct Chem

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“…[73][74][75][76][77] Furthermore, because of the negligible magnitude of charge-transfer (cf . Table I), we specifically focus on many-body effects of polarization-induced frequency shifts by comparing the frequency shift of NMA-(H 2 O) 3 complex with the sum of frequency shifts of three separate dimers.…”

Section: Many-body Effectsmentioning

confidence: 99%

Vibrational solvatochromism. II. A first-principle theory of solvation-induced vibrational frequency shift based on effective fragment potential method

Błasiak

Cho

2014

The Journal of Chemical Physics

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Vibrational solvatochromism is a solvation-induced effect on fundamental vibrational frequencies of molecules in solutions. Here we present a detailed first-principle coarse-grained theory of vibrational solvatochromism, which is an extension of our previous work [B. Błasiak, H. Lee, and M. Cho, J. Chem. Phys. 139(4), 044111 (2013)] by taking into account electrostatic, exchange-repulsion, polarization, and charge-transfer interactions. By applying our theory to the model N-methylacetamide-water clusters, solute-solvent interaction-induced effects on amide I vibrational frequency are fully elucidated at Hartree-Fock level. Although the electrostatic interaction between distributed multipole moments of solute and solvent molecules plays the dominant role, the contributions from exchange repulsion and induced dipole-electric field interactions are found to be of comparable importance in short distance range, whereas the charge-transfer effect is negligible. The overall frequency shifts calculated by taking into account the contributions of electrostatics, exchange-repulsion, and polarization terms are in quantitative agreement with ab initio results obtained at the Hartree-Fock level of theory.

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“…Interaction energy between PDE5 binding site representation and each inhibitor was calculated within Hybrid Variation-Perturbation Theory (HVPT) [50, 51] decomposition scheme as the sum of binding energy values obtained for amino acid residue-inhibitor dimers. Each amino acid residue included in particular dimers was considered separately except for residues linked by a peptide bond, i.e., Asp764 and Leu765, Ala767 and Ile768, as well as Ile778 and Ala779 residues.…”

Section: Methodsmentioning

confidence: 99%

Revisiting the halogen bonding between phosphodiesterase type 5 and its inhibitors

Jedwabny

Dyguda-Kazimierowicz

2019

J Mol Model

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Halogenated ligands are nowadays commonly designed in order to increase their potency against protein targets. Although novel computational methods of evaluating the affinity of such halogenated inhibitors have emerged, they still lack the sufficient accuracy, which is especially noticeable in the case of empirical scoring functions, being the method of choice in the drug design process. Here, we evaluated a series of halogenated inhibitors of phosphodiesterase type 5 with ab initio methods, revealing the physical nature of ligand binding and determining the components of interaction energy that are essential for proper inhibitor ranking. In particular, a nonempirical scoring model combining long-range contributions to the interaction energy provided a significant correlation with experimental binding potency, outperforming a number of commonly used empirical scoring functions. Considering the low computational cost associated with remarkable predictive abilities of the aforementioned model, it could be used for rapid assessment of the ligand affinity in the process of rational design of novel halogenated compounds.Electronic supplementary materialThe online version of this article (10.1007/s00894-018-3897-z) contains supplementary material, which is available to authorized users.

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The Nature of Interactions in the Ionic Crystal of 3-Pentenenitrile, 2-Nitro-5-oxo, Ion(−1), Sodium

Cited by 39 publications

References 49 publications

DFT studies on the structures and stabilities of N5 +-containing salts

DFT studies on the structures and stabilities of N5 +-containing salts

Vibrational solvatochromism. II. A first-principle theory of solvation-induced vibrational frequency shift based on effective fragment potential method

Revisiting the halogen bonding between phosphodiesterase type 5 and its inhibitors

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